Repositories list

• pubmlst_client

  Public
  List and download schemes from pubMLST.org and other BIGSDB servers

  bioinformaticsmlstrest-client

  Python

  •

  MIT License

  •5•8•0•1•Updated Oct 14, 2024Oct 14, 2024

• galaxy_tools

  Public
  toolsgenomicsmicrobial-genomics+ 2usegalaxygenomic-workflows

  Python

  •1•0•0•0•Updated Sep 19, 2023Sep 19, 2023

• irida-plugin-tbprofiler

  Public
  tuberculosisantimicrobial-resistanceirida-pipeline

  Java

  •

  Apache License 2.0

  •1•1•1•0•Updated Sep 19, 2023Sep 19, 2023

• irida-plugin-tbprofiler-multisample

  Public
  Java

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 13, 2023Jul 13, 2023

• irida-plugin-species-abundance

  Public
  Estimate the relative abundance of sequence reads originating from different species in a sample using the IRIDA system

  metagenomicsbioinformatics-pipelinemicrobial-genomics+ 3species-abundance-distributionsspecies-identificationirida-pipeline

  Java

  •

  Apache License 2.0

  •3•0•1•1•Updated Jun 2, 2023Jun 2, 2023

• compute_canada_cloud

  Public
  0•0•0•0•Updated Apr 29, 2021Apr 29, 2021

• snakemake_demo

  Public
  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Feb 25, 2021Feb 25, 2021

• decision-tree

  Public
  A question and answer web form system for exploring the research questions and datasets pertinent to an emerging infectious disease outbreak.

  Makefile

  •1•1•0•0•Updated Jan 15, 2021Jan 15, 2021

• irida-plugin-snippy-single

  Public
  Call SNPs and indels between a reference genome and your sequence data

  Java

  •0•0•2•0•Updated Nov 20, 2020Nov 20, 2020

• irida-plugin-snippy-phylogenomics

  Public
  Call core SNPs agains a reference genome for a set of bacterial isolates, and build a phylogenetic tree based on the core-genome SNP information.

  bioinformatics-pipelinemicrobial-genomicsphylogenomics-pipeline+ 1irida-pipeline

  Java

  •1•2•3•1•Updated Nov 20, 2020Nov 20, 2020

• COVID19-QC

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 10, 2020Nov 10, 2020

• irida-plugin-plasmid-screen

  Public
  bioinformatics-pipelineantimicrobial-resistanceplasmid-genomics+ 2galaxyirida-pipeline

  Java

  •0•0•1•1•Updated Oct 13, 2020Oct 13, 2020

• irida-plugin-tetyper

  Public
  Determine the sequence type of specific transposable elements in bacterial isolates.

  bioinformatics-pipelinemicrobial-genomicstransposable-elements+ 2galaxyirida-pipeline

  Java

  •

  Apache License 2.0

  •0•0•1•1•Updated Oct 13, 2020Oct 13, 2020

• irida-plugin-resistance-screen

  Public
  Detect the presence of specific resistance genes in a sample using the IRIDA system

  bioinformatics-pipelinemicrobial-genomicsantimicrobial-resistance+ 1irida-pipelines

  Java

  •

  Apache License 2.0

  •2•0•1•1•Updated Oct 13, 2020Oct 13, 2020

• lexmapr_ontology

  Public
  An ontology that contains various agency category schemes that Lexmapr can use to report matched terms by.

  Creative Commons Zero v1.0 Universal

  •1•0•0•1•Updated Aug 10, 2020Aug 10, 2020

• ontofetch

  Public
  Ontofetch is a command line tool to fetch branches of terms from a given local file or internet based ontology URL. This is output in JSON format, and includes term label, definition, broad, narrow, exact and unspecified) synonyms.

  Python

  •2•3•1•0•Updated Jun 24, 2020Jun 24, 2020

• irida-plugin-micall-lite

  Public
  Human RNA virus genotyping

  bioinformatics-pipelineviral-genomicsgalaxy+ 1irida-pipeline

  Java

  •

  Apache License 2.0

  •0•0•1•0•Updated Feb 28, 2020Feb 28, 2020

• blast_reporting

  Public
  A Galaxy tool that converts an NCBI BLAST XML format search result into 12, 24, 26 or custom column tabular and HTML reports.

  Python

  •

  Other

  •2•1•2•1•Updated Feb 27, 2020Feb 27, 2020

• purl.obolibrary.org

  Public
  A new system for managing OBO PURLs

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •128•0•0•0•Updated Dec 20, 2019Dec 20, 2019

• tutorial

  Public
  Protege tutorial resources

  Other

  •0•1•0•0•Updated Nov 15, 2019Nov 15, 2019

• flu_classification_suite

  Public
  💉 📊 Flu Classification Suite

  Python

  •1•4•2•0•Updated Nov 12, 2019Nov 12, 2019

• irida-plugin-mlst

  Public
  Determine the MLST sequence type for samples using PubMLST schemes in the IRIDA system

  bioinformatics-pipelinemicrobial-genomicsmlst+ 3microbial-subtypinggalaxyirida-pipeline

  Java

  •2•0•3•0•Updated Jun 20, 2019Jun 20, 2019

• cpo-pipeline

  Public
  An analysis pipeline for the purpose of investigating Carbapenemase-Producing Organisms.

  Python

  •

  MIT License

  •2•1•8•0•Updated Jun 14, 2019Jun 14, 2019

• sequdas-qc

  Public
  Python

  •

  MIT License

  •2•0•1•1•Updated Apr 30, 2019Apr 30, 2019

• software-development-best-practices

  Public
  0•0•0•0•Updated Apr 2, 2019Apr 2, 2019

• irida

  Public
  Canada’s Integrated Rapid Infectious Disease Analysis Platform for Genomic Epidemiology

  Java

  •

  Apache License 2.0

  •31•0•0•0•Updated Mar 20, 2019Mar 20, 2019

• sequdas-web

  Public
  Python

  •

  MIT License

  •0•0•3•1•Updated Mar 20, 2019Mar 20, 2019

• clade_assignment

  Public
  Python scripts to assign clade designations to influenza amino acid fasta files.

  Python

  •2•0•0•0•Updated Jan 8, 2019Jan 8, 2019

• routine-nanopore-processing

  Public
  Shell

  •

  GNU General Public License v3.0

  •1•0•1•0•Updated Jan 3, 2019Jan 3, 2019

• sequdas-uploader

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 4, 2018Dec 4, 2018